Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Processing Description
• Related Publications
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

CTD data were collected from the near surface to 5-10 m off the seafloor in the Salish Sea on R/V Rachel Carson cruises RC0078, RC0104, and RC0138 during 2022, 2023 and 2025. They were collected using a Sea-Bird SBE9 CTD profiler equipped with a pH sensor (SBE 18), oxygen sensor (SBE 43), fluorometer (WETLabs ECO-AFL), transmissometer (WETLabs C-Star), PAR sensor (LI-COR Biospherical PAR Sensor), and 12 Niskin bottles.

CTD data from near surface to 5-10 m off the seafloor were processed using Sea Bird software to create 1-m data bins. The .cnv files were exported as .csv files.

- Loaded 65 CSV files from the one_meter_binned directory using filenames as resource names; missing values defined as empty strings and "nd"
- Concatenated all 65 resources into a single resource named ctd_all, mapping fields: year_month_day, Cruise, Station, Cast, LAT, LON, PRS, Depth, TMP, SAL, OXY, OXYsat, Beam.Attenuation, Beam.Transmission, Fluorescence, PAR, pH, and file_name; source file paths added as new column path_name
- Applied find/replace on path_name to strip directory path, retaining only the filename (e.g., RC0078_S3_C2.csv)
- Renamed file_name to filename_cnv (contains .cnv filenames) and path_name to filename_csv (contains .csv filenames converted from original SBE .cnv CTD profile files)
- Reordered fields to move both filename fields to the end: Date, Cruise, Station, Cast, LAT, LON, PRS, Depth, TMP, SAL, OXY, OXYsat, Beam.Attenuation, Beam.Transmission, Fluorescence, PAR, pH, filename_cnv, filename_csv
- Renamed year_month_day to Date
- Renamed Beam.Attenuation to Beam_Attenuation and Beam.Transmission to Beam_Transmission by replacing dots with underscores
- Reordered fields to final column order: Date, Cruise, Station, LAT, LON, Cast, PRS, Depth, TMP, SAL, OXY, OXYsat, Beam_Attenuation, Beam_Transmission, Fluorescence, PAR, pH, filename_cnv, filename_csv
- Corrected LAT values at rows 2013 and 2014 by negating them (0 - LAT)
- Corrected LON value at row 2013 by negating it (0 - LON)
- Output written to 997362_v1_salish_sea_ctd.csv

NSF Award Abstract:
Photosynthetic microbes provide food for nearly all other life in the ocean. Their metabolism produces organic molecules called metabolites that can leak out of cells, be intentionally excreted into seawater, or be released during cell death. Once outside the cell, these metabolites are the basis for specific interactions among microbes and determine community structure and activity. Yet, current understanding of metabolites in the ocean is limited by a historical lack of ability to measure them. The work proposed here will expand current knowledge of metabolite structures, concentrations, and production rates using recently developed analytical methods. These methods have already led to the discovery that homarine, a substituted pyridine first found in lobster in 1933, is the most abundant detectable metabolite in microbial communities of the North Pacific Ocean. While homarine is known as a predator deterrent, osmoprotectant, methyl donor, and antibiofouling agent, studies of its role in microbial community dynamics are lacking. The work proposed will clarify the role of homarine in the ocean’s microbial communities. This work will create an open-source metabolite database that will serve the broader field of metabolomics, a growing area in environmental, engineering, and medical sciences. This collaboration will also promote the careers of a graduate student and a postdoctoral researcher as well as an early career professor from an underrepresented group at a primarily undergraduate institution (PUI). Undergraduates from both institutions will contribute to project development and implementation, local cruises on the R.V. Carson, lab work, and dissemination of results. This research will be integrated into a curriculum-based research experience for undergraduates in a 200-level genetics course at the PUI, University of Puget Sound.

The proposed work will carry out field studies and laboratory experiments to test the hypothesis that metabolites are quantitatively significant forms of carbon and nitrogen flowing through microbial communities. The identity, quantity, and production rates of metabolites will also be determined. For homarine, the enzymes and organisms responsible for its transformations will be determined. Specific proposed activities will 1) Quantify nitrogenous metabolite pools and their net production rates (particulate and dissolved) in phytoplankton cultures and in marine surface water communities; 2) Isolate homarine consuming heterotrophic bacteria and use mutagenesis techniques, transcriptomics, and stable isotope assisted metabolomics to annotate genes and characterize the biochemical reactions involved in the degradation of homarine; 3) Carry out incubations of stable isotope labeled homarine in phytoplankton cultures, heterotrophic bacterial cultures sensitive to homarine, and natural communities to quantitatively evaluate the effect of homarine on growth, track homarine through metabolic pathways, and determine the kinetics of homarine uptake; 4) Identify homarine consumers and biochemical pathways for homarine use in the environment by mining existing environmental metatranscriptomes for homarine catabolism genes. The combination of these approaches will provide better understanding of the flow of nitrogen containing metabolites through marine microbial ecosystems. Results from this work will be disseminated through peer reviewed open-source publications as well as presentations to the scientific community and the general public.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.